5QC8

Crystal structure of human Cathepsin-S with bound ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 
    0.198 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.169 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted BFVClick on this verticalbar to view details

This is version 2.3 of the entry. See complete history


Literature

Crystal structure of human Cathepsin-S with bound ligand

Bembenek, S.D.Ameriks, M.K.Mirzadegan, T.Yang, H.Shao, C.Burley, S.K.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cathepsin S
A, B
223Homo sapiensMutation(s): 1 
Gene Names: CTSS
EC: 3.4.22.27
UniProt & NIH Common Fund Data Resources
Find proteins for P25774 (Homo sapiens)
Explore P25774 
Go to UniProtKB:  P25774
PHAROS:  P25774
GTEx:  ENSG00000163131 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25774
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BFV
Query on BFV

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
N-benzyl-1-{3-[(2-chloro-5-{5-(methylsulfonyl)-1-[3-(morpholin-4-yl)propyl]-4,5,6,7-tetrahydro-1H-pyrazolo[4,3-c]pyridin-3-yl}phenyl)ethynyl]phenyl}methanamine
C36 H40 Cl N5 O3 S
LIGRCXVOYJUELL-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
BFV BindingDB:  5QC8 IC50: 290 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free:  0.198 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.169 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.062α = 90
b = 37.153β = 93.14
c = 127.677γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted BFVClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-02-21
    Changes: Structure summary
  • Version 2.0: 2018-06-06
    Changes: Atomic model, Data collection, Derived calculations, Other, Refinement description, Structure summary
  • Version 2.1: 2021-02-10
    Changes: Database references, Structure summary
  • Version 2.2: 2021-11-17
    Changes: Advisory, Database references, Structure summary
  • Version 2.3: 2024-10-23
    Changes: Data collection, Refinement description, Structure summary